Publications

Zhong, K., Nguyen, H. L., Do, T. N., Tan, H. S., Knoester, J., & Jansen, T. L. C. (2024). Coarse-Grained Approach to Simulate Signatures of Excitation Energy Transfer in Two-Dimensional Electronic Spectroscopy of Large Molecular Systems. Journal of Chemical Theory and Computation, 20(14), 6111-6124. https://doi.org/10.1021/acs.jctc.4c00413

Nguyen, H. L., Do, T. N., Zhong, K., Akhtar, P., Jansen, T. L. C., Knoester, J., Caffarri, S., Lambrev, P., & Tan, H. S. (2024). Inter-subunit energy transfer processes in a minimal plant photosystem II supercomplex. Science Advances, 10(8), Article eadh0911. https://doi.org/10.1126/sciadv.adh0911

Zhong, K., Nguyen, H. L., Do, T. N., Tan, H. S., Knoester, J., & Jansen, T. L. C. (2023). An efficient time-domain implementation of the multichromophoric Förster resonant energy transfer method. Journal of Chemical Physics, 158(6), 1710–1722. https://doi.org/10.1063/5.0136652

Manrho, M., Krishnaswamy, S. R., Kriete, B., Patmanidis, I., de Vries, A. H., Marrink, S. J., Jansen, T. L. C., Knoester, J., & Pshenichnikov, M. S. (2023). Watching Molecular Nanotubes Self-Assemble in Real Time. Journal of the American Chemical Society, 145(41), 22494–22503. https://doi.org/10.1021/jacs.3c07103

Manrho, M., Jansen, T. L. C., & Knoester, J. (2022). Optical signatures of the coupling between excitons and charge transfer states in linear molecular aggregates. Journal of Chemical Physics, 156(22), Article 224112. https://doi.org/10.1063/5.0095470

Bernhardt, R., Manrho, M., Zablocki, J., Rieland, L., Lützen, A., Schiek, M., Meerholz, K., Zhu, J., Jansen, T. L. C., Knoester, J., & Van Loosdrecht, P. H. M. (2022). Structural Disorder as the Origin of Optical Properties and Spectral Dynamics in Squaraine Nano-Aggregates. Journal of the American Chemical Society, 144(42), 19372–19381. https://doi.org/10.1021/jacs.2c07064

Nhut, T., Nguyen, H. L., Akhtar, P., Zhong, K., Jansen, T. L. C., Knoester, J., Caffarri, S., Lambrev, P. H., & Tan, H.-S. (2022). Ultrafast Excitation Energy Transfer Dynamics in the LHCII–CP29–CP24 Subdomain of Plant Photosystem II. The Journal of Physical Chemistry Letters, 13(19), 4263–4271. https://doi.org/10.1021/acs.jpclett.2c00194

Nguyen, H. L., Do, T. N., Akhtar, P., Jansen, T. L. C., Knoester, J., Wang, W., Shen, J.-R., Lambrev, P. H., & Tan, H.-S. (2021). An Exciton Dynamics Model of Bryopsis corticulans Light-Harvesting Complex II. Journal of Physical Chemistry B, 125(4), 1134-1143. https://doi.org/10.1021/acs.jpcb.0c10634

Günther, L. M., Knoester, J., & Köhler, J. (2021). Limitations of linear dichroism spectroscopy for elucidating structural issues of light-harvesting aggregates in chlorosomes. Molecules, 26(4), Article 899. https://doi.org/10.3390/molecules26040899

Kunsel, T., Günther, L. M., Köhler, J., Jansen, T. L. C., & Knoester, J. (2021). Probing size variations of molecular aggregates inside chlorosomes using single-object spectroscopy. Journal of Chemical Physics, 155(12), Article 124310. https://doi.org/10.1063/5.0061529

Kunsel, T., Jansen, T. L. C., & Knoester, J. (2021). Scaling relations of exciton diffusion in linear aggregates with static and dynamic disorder. Journal of Chemical Physics, 155(13), Article 134305. https://doi.org/10.1063/5.0065206

Bondarenko, A. S., Knoester, J., & Jansen, T. L. C. (2020). Comparison of methods to study excitation energy transfer in molecular multichromophoric systems. Chemical Physics, 529, Article 110478. https://doi.org/10.1016/j.chemphys.2019.110478

Bondarenko, A. S., Jansen, T. L. C., & Knoester, J. (2020). Exciton localization in tubular molecular aggregates: Size effects and optical response. Journal of Chemical Physics, 152(19), Article 194302. https://doi.org/10.1063/5.0008688

Kriete, B., Bondarenko, A. S., Alessandri, R., Patmanidis, I., Krasnikov, V. V., Jansen, T. L. C., Marrink, S. J., Knoester, J., & Pshenichnikov, M. S. (2020). Molecular versus excitonic disorder in individual artificial light-harvesting systems. Journal of the American Chemical Society, 142(42), 18073-18085. Article jacs.0c07392. https://doi.org/10.1021/jacs.0c07392

Bondarenko, A. S., Patmanidis, I., Alessandri, R., Souza, P. C. T., Jansen, T. L. C., de Vries, A. H., Marrink, S. J., & Knoester, J. (2020). Multiscale modeling of molecular structure and optical properties of complex supramolecular aggregates. Chemical Science, 11(42), 11514-11524. https://doi.org/10.1039/d0sc03110k

Nugroho, B. S., Iskandar, A. A., Malyshev, V. A., & Knoester, J. (2020). Plasmon-assisted two-photon absorption in a semiconductor quantum dot-metallic nanoshell composite. Physical Review B, 102(4), Article 045405. https://doi.org/10.1103/PhysRevB.102.045405

Kunsel, T., Loehner, A., Mayo, J. J., Koehler, J., Jansen, T. L. C., & Knoester, J. (2020). Unraveling intra-aggregate structural disorder using single-molecule spectroscopy. Journal of Chemical Physics, 153(13), Article 134304. https://doi.org/10.1063/5.0023551

Kriete, B., Luettig, J., Kunsel, T., Maly, P., Jansen, T. L. C., Knoester, J., Brixner, T., & Pshenichnikov, M. S. (2019). Interplay between structural hierarchy and exciton diffusion in artificial light harvesting. Nature Communications, 10, Article 4615. https://doi.org/10.1038/s41467-019-12345-9

Nugroho, B. S., Iskandar, A. A., Malyshev, V. A., & Knoester, J. (2019). Plasmon-assisted two-photon Rabi oscillations in a semiconductor quantum dot - metal nanoparticle heterodimer. Physical Review B, 99(7), Article 075302. https://doi.org/10.1103/PhysRevB.99.075302

Loehner, A., Kunsel, T., Roehr, M. I. S., Jansen, T. L. C., Sengupta, S., Wuerthner, F., Knoester, J., & Koehler, J. (2019). Spectral and Structural Variations of Biomimetic Light-Harvesting Nanotubes. JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 10(11), 2715-2724. https://doi.org/10.1021/acs.jpclett.9b00303

Thyrhaug, E., Tempelaar, R., Alcocer, M. J. P., Zidek, K., Bina, D., Knoester, J., Jansen, T. L. C., & Zigmantas, D. (2018). Identification and characterization of diverse coherences in the Fenna-Matthews-Olson complex. Nature Chemistry, 10(7), 780-786. https://doi.org/10.1038/s41557-018-0060-5

Guenther, L. M., Loehner, A., Reiher, C., Kunsel, T., Jansen, T. L. C., Tank, M., Bryant, D. A., Knoester, J., & Koehler, J. (2018). Structural Variations in Chlorosomes from Wild-Type and a bchQR Mutant of Chlorobaculum tepidum Revealed by Single-Molecule Spectroscopy. Journal of Physical Chemistry B, 122(26), 6712-6723. https://doi.org/10.1021/acs.jpcb.8b02875

Farag, M. H., Jansen, T. L. C., & Knoester, J. (2018). The origin of absorptive features in the two-dimensional electronic spectra of rhodopsin. PPCP : Physical Chemistry Chemical Physics, 20(18), 12746-12754. https://doi.org/10.1039/c8cp00638e

Compaijen, P. J., Malyshev, V. A., & Knoester, J. (2018). Time-dependent transport of a localized surface plasmon through a linear array of metal nanoparticles: Precursor and normal mode contributions. Physical Review. B: Condensed Matter and Materials Physics, 97(8), Article 085428. https://doi.org/10.1103/PhysRevB.97.085428

Guenther, L. M., Jendrny, M., Bloemsma, E. A., Tank, M., Oostergetel, G. T., Bryant, D. A., Knoester, J., & Kohler, J. (2017). Correction to “Structure of Light-Harvesting Aggregates in Individual Chlorosomes”. Journal of Physical Chemistry B, 121(23), 5882. https://doi.org/10.1021/acs.jpcb.7b04945

Wan, Y., Stradomska, A., Knoester, J., & Huang, L. (2017). Direct Imaging of Exciton Transport in Tubular Porphyrin Aggregates by Ultrafast Microscopy. Journal of the American Chemical Society, 139(21), 7287-7293. https://doi.org/10.1021/jacs.7b01550

Tempelaar, R., Jansen, T. L. C., & Knoester, J. (2017). Exciton-Exciton Annihilation Is Coherently Suppressed in H-Aggregates, but Not in J-Aggregates. The Journal of Physical Chemistry Letters, 8(24), 6113-6117. https://doi.org/10.1021/acs.jpclett.7b02745, https://doi.org/10.48550/arxiv.1705.05861

Farag, M. H., Hoenders, B. J., Knoester, J., & Jansen, T. L. C. (2017). Spectral line shapes in linear absorption and two-dimensional spectroscopy with skewed frequency distributions. Journal of Chemical Physics, 146(23), Article 234201. https://doi.org/10.1063/1.4985665

Kriete, B., Bondarenko, A. S., Jumde, V. R., Franken, L. E., Minnaard, A. J., Jansen, T. L. C., Knoester, J., & Pshenichnikov, M. S. (2017). Steering Self-Assembly of Amphiphilic Molecular Nanostructures via Halogen Exchange. The Journal of Physical Chemistry Letters, 8(13), 2895-2901. https://doi.org/10.1021/acs.jpclett.7b00967

Johnson, P. J. M., Farag, M. H., Halpin, A., Morizumi, T., Prokhorenko, V. I., Knoester, J., Jansen, T. L. C., Ernst, O. P., & Miller, R. J. D. (2017). The Primary Photochemistry of Vision Occurs at the Molecular Speed Limit. The Journal of Physical Chemistry. B: Materials, Surfaces, Interfaces, & Biophysical, 121(16), 4040-4047. https://doi.org/10.1021/acs.jpcb.7b02329

Nugroho, B. S., Iskandar, A. A., Malyshev, V. A., & Knoester, J. (2017). Instabilities in the optical response of a semiconductor quantum dot-metal nanoparticle heterodimer: self-oscillations and chaos. Journal of Optics, 19(1), Article 015004. https://doi.org/10.1088/2040-8986/19/1/015004

Tempelaar, R., Koster, J. A., Havenith, R., Knoester, J., & Jansen, T. (2016). Charge recombination suppressed by destructive quantum interference in heterojunction materials. Abstracts of Papers of the American Chemical Society, 252.

Tempelaar, R., Koster, L. J. A., Havenith, R. W. A., Knoester, J., & Jansen, T. L. C. (2016). Charge Recombination Suppressed by Destructive Quantum Interference in Heterojunction Materials. The Journal of Physical Chemistry Letters, 7(1), 198-203. https://doi.org/10.1021/acs.jpclett.5b02580

Tempelaar, R., Koster, L. J. A., Havenith, R. W. A., Knoester, J., & Jansen, T. L. C. (2016). Correction to “Charge Recombination Suppressed by Destructive Quantum Interference in Heterojunction Materials”. The Journal of Physical Chemistry Letters, 7(18), 3659-3659. https://doi.org/10.1021/acs.jpclett.6b01956

Compaijen, P. J., Malyshev, V. A., & Knoester, J. (2016). Elliptically polarized modes for the unidirectional excitation of surface plasmon polaritons. Optics Express, 24(4), 3858-3872. https://doi.org/10.1364/OE.24.003858

Dijkstra, A. G., Duan, H.-G., Knoester, J., Nelson, K. A., & Cao, J. (2016). How two-dimensional brick layer J-aggregates differ from linear ones: Excitonic properties and line broadening mechanisms. Journal of Chemical Physics, 144(13), Article 134310. https://doi.org/10.1063/1.4944980

Tempelaar, R., Halpin, A., Johnson, P. J. M., Cai, J., Murphy, R. S., Knoester, J., Miller, R. J. D., & Jansen, T. L. C. (2016). Laser-Limited Signatures of Quantum Coherence. The Journal of Physical Chemistry. A: Molecules, Spectroscopy, Kinetics, Environment, & General Theory, 120(19), 3042-3048. https://doi.org/10.1021/acs.jpca.5b10312

Farag, M. H., Jansen, T. L. C., & Knoester, J. (2016). Probing the Interstate Coupling near a Conical Intersection by Optical Spectroscopy. The Journal of Physical Chemistry Letters, 7(17), 3328-3334. https://doi.org/10.1021/acs.jpclett.6b01463

Chuang, C., Lee, C. K., Moix, J. M., Knoester, J., & Cao, J. (2016). Quantum Diffusion on Molecular Tubes: Universal Scaling of the 1D to 2D Transition. Physical Review Letters, 116(19), Article 196803. https://doi.org/10.1103/PhysRevLett.116.196803

Guenther, L. M., Jendrny, M., Bloemsma, E. A., Tank, M., Oostergetel, G. T., Bryant, D. A., Knoester, J., & Koehler, J. (2016). Structure of Light-Harvesting Aggregates in Individual Chlorosomes. The Journal of Physical Chemistry. B: Materials, Surfaces, Interfaces, & Biophysical, 120(24), 5367-5376. https://doi.org/10.1021/acs.jpcb.6b03718

Bloemsma, E. A., Silvis, M. H., Stradomska, A., & Knoester, J. (2016). Vibronic effects and destruction of exciton coherence in optical spectra of J-aggregates: A variational polaron transformation approach. Chemical Physics, 481, 250-261. https://doi.org/10.1016/j.chemphys.2016.06.018

van der Vegte, N., Prajapati, J., Kleinekathoefer, U., Knoester, J., & Jansen, T. (2015). Atomistic Modeling of Two-Dimensional Electronic Spectra and Excited State Dynamics for a Light Harvesting 2 Complex. The Journal of Physical Chemistry B, 119(4), 1302–1313. https://doi.org/10.1021/jp509247p

Compaijen, P. J., Malyshev, V. A., & Knoester, J. (2015). Engineering plasmon dispersion relations: hybrid nanoparticle chain - substrate plasmon polaritons. Optics Express, 23(3), 2280-2292. https://doi.org/10.1364/OE.23.002280

Hestand, N. J., Tempelaar, R., Knoester, J., Jansen, T. L. C., & Spano, F. C. (2015). Exciton mobility control through sub − Å packing modifications in molecular crystals. Physical Review. B: Condensed Matter and Materials Physics, 91(19), Article 195315. https://doi.org/10.1103/PhysRevB.91.195315

Broer, W., Waalkens, H., Svetovoy, V., Knoester, J., & Palasantzas, G. (2015). Nonlinear Actuation Dynamics of Driven Casimir Oscillators with Rough Surfaces. Physical Review Applied, 4(5), Article 054016. https://doi.org/10.1103/PhysRevApplied.4.054016

Bloemsma, E. A., Vlaming, S. M., Malyshev, V. A., & Knoester, J. (2015). Signature of Anomalous Exciton Localization in the Optical Response of Self-Assembled Organic Nanotubes. Physical Review Letters, 114(15), Article 156804. https://doi.org/10.1103/PhysRevLett.114.156804

Nugroho, B. S., Malyshev, V. A., & Knoester, J. (2015). Tailoring optical response of a hybrid comprising a quantum dimer emitter strongly coupled to a metallic nanoparticle. Physical Review B, 92(16), Article 165432. https://doi.org/10.1103/PhysRevB.92.165432

Wan, Y., Stradomska, A., Fong, S., Guo, Z., Schaller, R. D., Wiederrecht, G. P., Knoester, J., & Huang, L. (2014). Exciton Level Structure and Dynamics in Tubular Porphyrin Aggregates. The Journal of Physical Chemistry. C: Nanomaterials and Interfaces, 118(43), 24854-24865. https://doi.org/10.1021/jp507435a

Haverkort, F., Stradomska, A., Vries, A. H. D., & Knoester, J. (2014). First-Principles Calculation of the Optical Properties of an Amphiphilic Cyanine Dye Aggregate. The Journal of Physical Chemistry. A: Molecules, Spectroscopy, Kinetics, Environment, & General Theory, 118(6), 1012-1023. https://doi.org/10.1021/jp4112487

Haverkort, F., Stradomska, A., & Knoester, J. (2014). First-Principles Simulations of the Initial Phase of Self-Aggregation of a Cyanine Dye: Structure and Optical Spectra. The Journal of Physical Chemistry. B: Materials, Surfaces, Interfaces, & Biophysical, 118(29), 8877-8890. https://doi.org/10.1021/jp5049277

Jumper, C. C., Anna, J. M., Stradomska, A., Schins, J., Myahkostupov, M., Prusakova, V., Oblinsky, D. G., Castellano, F. N., Knoester, J., & Scholes, G. D. (2014). Intramolecular radiationless transitions dominate exciton relaxation dynamics. Chemical Physics Letters, 599, 23-33. https://doi.org/10.1016/j.cplett.2014.03.007

Tempelaar, R., Spano, F. C., Knoester, J., & Jansen, T. L. C. (2014). Mapping the Evolution of Spatial Exciton Coherence through Time-Resolved Fluorescence. The Journal of Physical Chemistry Letters, 5(9), 1505-1510. https://doi.org/10.1021/jz500488u

van der Vegte, C. P., Knop, S., Voehringer, P., Knoester, J., & Jansen, T. L. C. (2014). OH-Stretching in Synthetic Hydrogen-Bonded Chains. The Journal of Physical Chemistry B, 118(23), 6256-6264. https://doi.org/10.1021/jp504267h

Eisele, D. M., Arias, D. H., Fu, X., Bloemsma, E. A., Steiner, C. P., Jensen, R. A., Rebentrost, P., Eisele, H., Tokmakoff, A., Lloyd, S., Nelson, K. A., Nicastro, D., Knoester, J., & Bawendi, M. G. (2014). Robust excitons inhabit soft supramolecular nanotubes. Proceedings of the National Academy of Science of the United States of America, 111(33), E3367-E3375. https://doi.org/10.1073/pnas.1408342111

Chuang, C., Knoester, J., & Cao, J. (2014). Scaling Relations and Optimization of Excitonic Energy Transfer Rates between One-Dimensional Molecular Aggregates. The Journal of Physical Chemistry. B: Materials, Surfaces, Interfaces, & Biophysical, 118(28), 7827-7834. https://doi.org/10.1021/jp4124502

Halpin, A., Johnson, P. J. M., Tempelaar, R., Murphy, R. S., Knoester, J., Jansen, T. L. C., & Miller, R. J. D. (2014). Two-dimensional spectroscopy of a molecular dimer unveils the effects of vibronic coupling on exciton coherences. Nature Chemistry, 6(3), 196-201. https://doi.org/10.1038/NCHEM.1834

Tempelaar, R., Jansen, T. L. C., & Knoester, J. (2014). Vibrational Beatings Conceal Evidence of Electronic Coherence in the FMO Light-Harvesting Complex. The Journal of Physical Chemistry B, 118(45), 12865-12872. https://doi.org/10.1021/jp510074q

Tempelaar, R., Stradomska, A., Knoester, J., & Spano, F. C. (2013). Anatomy of an Exciton: Vibrational Distortion and Exciton Coherence in H- and J-Aggregates. Journal of Physical Chemistry B, 117(1), 457-466. https://doi.org/10.1021/jp310298n

Nugroho, B., Iskandar, A., Malyshev, V. A., & Knoester, J. (2013). Bistable optical response of a nanoparticle heterodimer: Mechanism, phase diagram, and switching time. Journal of Chemical Physics, 139(1), 014303-1-014303-8. Article 014303. https://doi.org/10.1063/1.4811181

van der Vegte, C. P., Dijkstra, A. G., Knoester, J., & Jansen, T. L. C. (2013). Calculating Two-Dimensional Spectra with the Mixed Quantum-Classical Ehrenfest Method. The Journal of Physical Chemistry A, 117(29), 5970-5980. https://doi.org/10.1021/jp311668r

Haverkort, F., Stradomska, A., de Vries, A. H., & Knoester, J. (2013). Investigating the Structure of Aggregates of an Amphiphilic Cyanine Dye with Molecular Dynamics Simulations. Journal of Physical Chemistry B, 117(19), 5857-5867. https://doi.org/10.1021/jp4005696

Munarriz, J., Malyshev, A. V., Malyshev, V. A., & Knoester, J. (2013). Optical Nanoantennas with Tunable Radiation Patterns. Nano Letters, 13(2), 444-450. https://doi.org/10.1021/nl303815a

Broer, W., Palasantzas, G., Knoester, J., & Svetovoy, V. B. (2013). Significance of the Casimir force and surface roughness for actuation dynamics of MEMS. Physical Review. B: Condensed Matter and Materials Physics, 87(12), 125413-1-125413-7. https://doi.org/10.1103/PhysRevB.87.125413

Vlaming, S. M., Malyshev, V. A., Eisfeld, A., & Knoester, J. (2013). Subdiffusive exciton motion in systems with heavy-tailed disorder. Journal of Chemical Physics, 138(21), 214316-1-214316-10. Article 214316. https://doi.org/10.1063/1.4808155

Tempelaar, R., van der Vegte, C. P., Knoester, J., & Jansen, T. L. C. (2013). Surface hopping modeling of two-dimensional spectra. Journal of Chemical Physics, 138(16), 164106-1-164106-10. Article 164106. https://doi.org/10.1063/1.4801519

Compaijen, P. J., Malyshev, V. A., & Knoester, J. (2013). Surface-mediated light transmission in metal nanoparticle chains. Physical Review. B: Condensed Matter and Materials Physics, 87(20), 205437-1-205437-7. Article 205437. https://doi.org/10.1103/PhysRevB.87.205437

Liang, C., Louhivuori, M., Marrink, S. J., Jansen, T. L. C., & Knoester, J. (2013). Vibrational Spectra of a Mechanosensitive Channel. JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 4(3), 448-452. https://doi.org/10.1021/jz3019258

Eisfeld, A., Vlaming, S. M., Moebius, S., Malyshev, V. A., & Knoester, J. (2012). Comment on "Excitons in Molecular Aggregates with Levy-Type Disorder: Anomalous Localization and Exchange Broadening of Optical Spectra" Reply. Physical Review Letters, 109(25), 259702-1-259702-1. Article 259702. https://doi.org/10.1103/PhysRevLett.109.259702

Jansen, T. L. C., Dijkstra, A. G., Watson, T. M., Hirst, J. D., & Knoester, J. (2012). Erratum: “Modeling the amide I bands of small peptides” [J. Chem. Phys. 125, 044312 (2006)]. Journal of Chemical Physics, 136(20), Article 209901. https://doi.org/10.1063/1.4722584

Lessing, J., Roy, S., Reppert, M., Baer, M., Marx, D., Jansen, T. L. C., Knoester, J., & Tokmakoff, A. (2012). Identifying Residual Structure in Intrinsically Disordered Systems: A 2D IR Spectroscopic Study of the GVGXPGVG Peptide. Journal of the American Chemical Society, 134(11), 5032-5035. https://doi.org/10.1021/ja2114135

Bloemsma, E. A., & Knoester, J. (2012). Photon emission statistics and photon tracking in single-molecule spectroscopy of molecular aggregates: Dimers and trimers. Journal of Chemical Physics, 136(22), 224507-1-224507-14. Article 224507. https://doi.org/10.1063/1.4719210

Liang, C., Knoester, J., & Jansen, T. L. C. (2012). Proton Transport in a Membrane Protein Channel: Two-Dimensional Infrared Spectrum Modeling. Journal of Physical Chemistry B, 116(22), 6336-6345. https://doi.org/10.1021/jp3019827

Broer, W., Palasantzas, G., Knoester, J., & Svetovoy, V. B. (2012). Roughness correction to the Casimir force at short separations: Contact distance and extreme value statistics. Physical Review. B: Condensed Matter and Materials Physics, 85(15), Article 155410. https://doi.org/10.1103/PhysRevB.85.155410

Eisele, D. M., Cone, C. W., Bloemsma, E. A., Vlaming, S. M., van der Kwaak, C. G. F., Silbey, R. J., Bawendi, M. G., Knoester, J., Rabe, J. P., & Vanden Bout, D. A. (2012). Utilizing redox-chemistry to elucidate the nature of exciton transitions in supramolecular dye nanotubes. Nature Chemistry, 4(8), 655-662. https://doi.org/10.1038/NCHEM.1380

Tempelaar, R., Stradomska, A., Knoester, J., & Spano, F. C. (2011). Circularly Polarized Luminescence as a Probe for Long-Range Interactions in Molecular Aggregates. Journal of Physical Chemistry B, 115(36), 10592-10603. https://doi.org/10.1021/jp2053019

Vlaming, S. M., Bloemsma, E. A., Nietiadi, M. L., & Knoester, J. (2011). Disorder-induced exciton localization and violation of optical selection rules in supramolecular nanotubes. Journal of Chemical Physics, 134(11), 114507-1-114507-11. Article 114507. https://doi.org/10.1063/1.3528993

Marocico, C. A., & Knoester, J. (2011). Effect of surface-plasmon polaritons on spontaneous emission and intermolecular energy-transfer rates in multilayered geometries. Physical Review A, 84(5), 053824-1-053824-11. Article 053824. https://doi.org/10.1103/PhysRevA.84.053824

Olbrich, C., Jansen, T. L. C., Liebers, J., Aghtar, M., Struempfer, J., Schulten, K., Knoester, J., Kleinekathoefer, U., & Strümpfer, J. (2011). From Atomistic Modeling to Excitation Transfer and Two-Dimensional Spectra of the FMO Light-Harvesting Complex. Journal of Physical Chemistry B, 115(26), 8609-8621. https://doi.org/10.1021/jp202619a

Dijkstra, A. G., Jansen, T. L. C., & Knoester, J. (2011). Modeling the Vibrational Dynamics and Nonlinear Infrared Spectra of Coupled Amide I and II Modes in Peptides. Journal of Physical Chemistry B, 115(18), 5392-5401. https://doi.org/10.1021/jp109431a

Liang, C., Jansen, T. L. C., & Knoester, J. (2011). Proton transport in biological systems can be probed by two-dimensional infrared spectroscopy. Journal of Chemical Physics, 134(4), 044502-1-044502-8. Article 044502. https://doi.org/10.1063/1.3522770

Broer, W., Palasantzas, G., Knoester, J., & Svetovoy, V. B. (2011). Roughness correction to the Casimir force beyond perturbation theory. Europhysics Letters, 95(3), 30001-p1-30001-p6. Article 30001. https://doi.org/10.1209/0295-5075/95/30001

Roy, S., Lessing, J., Meisl, G., Ganim, Z., Tokmakoff, A., Knoester, J., & Jansen, T. L. C. (2011). Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline. Journal of Chemical Physics, 135(23), 234507-1-234507-11. Article 234507. https://doi.org/10.1063/1.3665417

Chernyak, V. Y., Knoester, J., & Tretiak, S. (2011). Tribute to Shaul Mukamel. Journal of Physical Chemistry B, 115(18), 5037-5038. https://doi.org/10.1021/jp202931j

Eisfeld, A., Vlaming, S. M., Malyshev, V. A., & Knoester, J. (2010). Excitons in Molecular Aggregates with Lévy-Type Disorder: Anomalous Localization and Exchange Broadening of Optical Spectra. Physical Review Letters, 105(13), 137402-1-137402-4. Article 137402. https://doi.org/10.1103/PhysRevLett.105.137402

Smith, A. W., Lessing, J., Ganim, Z., Peng, C. S., Tokmakoff, A., Roy, S., Jansen, T. L. C., & Knoester, J. (2010). Melting of a beta-Hairpin Peptide Using Isotope-Edited 2D IR Spectroscopy and Simulations. Journal of Physical Chemistry B, 114(34), 10913-10924. https://doi.org/10.1021/jp104017h

Augulis, R., Malyshev, A. V., Malyshev, V. A., Pugzlys, A., Knoester, J., & van Loosdrecht, P. H. M. (2010). Quest for Order in Chaos: Hidden Repulsive Level Statistics in Disordered Quantum Nanoaggregates. JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 1(19), 2911-2916. https://doi.org/10.1021/jz101003j

Stradomska, A., & Knoester, J. (2010). Shape of the Q band in the absorption spectra of porphyrin nanotubes: Vibronic coupling or exciton effects? Journal of Chemical Physics, 133(9), 094701-1-094701-10. Article 094701. https://doi.org/10.1063/1.3481654

Roy, S., Jansen, T. L. C., & Knoester, J. (2010). Structural classification of the amide I sites of a beta-hairpin with isotope label 2DIR spectroscopy. Physical Chemistry Chemical Physics, 12(32), 9347-9357. https://doi.org/10.1039/b925645h

Dijkstra, A. G., Jansen, T. L. C., & Knoester, J. (2010). Two-Dimensional Spectroscopy of Extended Molecular Systems: Applications to Energy Transport and Relaxation in an alpha-Helix. The Journal of Physical Chemistry A, 114(27), 7315-7320. https://doi.org/10.1021/jp9111124

Dykstra, T. E., Hennebicq, E., Beljonne, D., Gierschner, J., Claudio, G., Bittner, E. R., Knoester, J., & Scholes, G. D. (2009). Conformational Disorder and Ultrafast Exciton Relaxation in PPV-family Conjugated Polymers. Journal of Physical Chemistry B, 113(3), 656-667. https://doi.org/10.1021/jp807249b

Vlaming, S. M., Augulis, R., Stuart, M. C. A., Knoester, J., & van Loosdrecht, P. H. M. (2009). Exciton spectra and the microscopic structure of self-assembled porphyrin nanotubes. Journal of Physical Chemistry B, 113(8), 2273-2283. https://doi.org/10.1021/jp808235c

Marocico, C. A., & Knoester, J. (2009). Intermolecular resonance energy transfer in the presence of a dielectric cylinder. Physical Review A, 79(5), 053816-1-053816-15. Article 053816. https://doi.org/10.1103/PhysRevA.79.053816

Vlaming, S., Malyshev, V. A., & Knoester, J. (2009). Localization properties of one-dimensional Frenkel excitons: Gaussian versus Lorentzian diagonal disorder. Physical Review. B: Condensed Matter and Materials Physics, 79(20), 205121-1-205121-8. Article 205121. https://doi.org/10.1103/PhysRevB.79.205121

Eisele, D. M., Knoester, J., Kirstein, S., Rabe, J. P., Vanden Bout, D. A., & Rabe, J. P. (2009). Uniform exciton fluorescence from individual molecular nanotubes immobilized on solid substrates. Nature Nanotechnology, 4(10), 658-663. https://doi.org/10.1038/nnano.2009.227

Jansen, T. L. C., & Knoester, J. (2009). Waiting Time Dynamics in Two-Dimensional Infrared Spectroscopy. Accounts of Chemical Research, 42(9), 1405-1411. https://doi.org/10.1021/ar900025a

Malyshev, A., Malyshev, V., & Knoester, J. (2008). Frequency-controlled localization of optical signals in graded plasmonic chains. Nano Letters, 8(8), 2369-2372. https://doi.org/10.1021/nl8011962

Klugkist, J., Malyshev, V., & Knoester, J. (2008). Intrinsic optical bistability of thin films of linear molecular aggregates: The two-exciton approximation. Journal of Chemical Physics, 128(8), Article 084706. https://doi.org/10.1063/1.2832312

Dijkstra, A. G., Jansen, T. L. C., & Knoester, J. (2008). Localization and coherent dynamics of excitons in the two-dimensional optical spectrum of molecular J-aggregates. Journal of Chemical Physics, 128(16), Article 164511. https://doi.org/10.1063/1.2897753